The study of biological systems in their real environmental conditions is crucial to decipher the true image of structures and processes underlying their functionality. In this regard, development of non‐invasive optical techniques that do not require labelling, such as the investigation of tissue endogenous fluorescence, is particularly important and, as reflected in the increasing number of contributions published recently on this subject, was recognized by many leading groups. Multi‐spectral and lifetime detection of fluorescence provides an effective experimental tool to discriminate between multiple naturally‐occurring fluorophores in living tissues. At the same time, however, data analysis allowing us to understand the spectral, temporal and spatial information gathered, describing individual molecules involved in the autofluorescence of intact biological systems, represents a tough scientific challenge that has not yet been fully resolved. In this review, we discuss the latest advances in technologies that record and assess spectrally‐resolved fluorescence lifetime data as well as their biological and clinical applications. We show how these methods provide efficient sensing of molecules correlated with changes in the mitochondrial metabolic redox state in pathological conditions and/or of cell ultrastructures in diseased tissue, based on the presence of oxidation/reductionsensitive fluorophores and/or cell‐specific chromophores. Future directions are also outlined. (© 2009 by Astro Ltd., Published exclusively by WILEY‐VCH Verlag GmbH & Co. KGaA)